Tested with CCleaner v4.19.4867 on Win 7 64-bit: if "Session" is unticked for Google Chrome cleaning settings, and CCleaner is allowed to close Chrome during cleaning, all session windows will be lost apart from one. I imagine Piriform only tested Chrome session restore with a single window.
This issue doesn't occur if Chrome is exited manually (Tools > Exit) before running CCleaner (but it's not reasonable to expect users to remember to do that each time). Disabling the "Internet History" item for Chrome does *not* avoid the problem. Firefox and IE are unaffected - the former restores all windows fine, the latter isn't forced to close during cleaning.
Please could this issue be resolved - it affects any CCleaner user that keeps more than one Chrome window open. Thanks!
Related bug report: http://forum.piriform.com/?showtopic=41186